Identification of Key Genes Affecting Results of Hyperthermia in Osteosarcoma Based on Integrative ChIP-Seq/TargetScan Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28453502", "kind": "science-record", "revision": 7, "content_hash": "sha256:3ea859283e826353ae3857f40de10dcf1f0380defc281597d472b49460ee39c0", "created_at": "2026-11-01T15:40:25Z", "updated_at": "2026-11-01T21:20:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Key Genes Affecting Results of Hyperthermia in Osteosarcoma Based on Integrative ChIP-Seq/TargetScan Analysis.", "doi": "10.12659/msm.901191", "pmid": "28453502", "authors": ["Yuxia Shi", "Fan Yang", "Shuqing Wei", "Gang Xu"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2017, "abstract": "BACKGROUND The purpose of this study was to research the effects of hyperthermia on osteosarcoma (OS) by integrating the Chromatin Immunoprecipitation with the generation sequencing (ChIP-Seq) and TargetScan analysis of heat shock transcription factor 1 (HSF1). MATERIAL AND METHODS The HSF1 ChIP-seq dataset of GSE60984 was downloaded from the Gene Expressed Omnibus (GEO) database. The HSF1-binding sites were screened by MACS2 in OS cells after 10 and 20 min of hyperthermia, and they were annotated using the ChIPseeker package. The overlapped genes were selected out when HSF1-binding sites were located in the promoter region. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the overlaps. The miRNA-gene pairs of the overlaps were screened out via TargetScan, and the miRNA-gene-regulated network was constructed by Cytoscape software. RESULTS 1880 and 1283 genes of promoter regions were obtained in the osteosarcoma cells after 10 and 20 min of hyperthermia, respectively, and 889 of them were overlapped. The overlapped genes were enriched in 122 GO terms and 3 KEGG pathways. There were 13 657 pairs involved in the miRNA-gene regulated network of the overlaps. CONCLUSIONS Some biomarkers were identified for OS treated with hyperthermia. Moreover, some GO terms (regulation of programmed cell death and regulation of cell death) and pathways (p53 signaling pathway, methane metabolism, and viral myocarditis) might be involved.", "claims": [{"id": "claim-method", "statement": "In this study it was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the above overlaps. Moreover, the GO terms and KEGG pathways were selected out with the criteria of P value <0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28453502", "locator": "sections[6] \"Functional and pathway enrichment analysis of overlaps\" paragraph 2", "quote": "In this study it was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the above overlaps. Moreover, the GO terms and KEGG pathways were selected out with the criteria of P value <0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In this dataset, there were 3 samples of OS cell: one was treated with both anti-HSF1 antibody and heat shocked for 10 min, another was treated with anti-HSF1 antibody and was heat shocked for 20 min, and the last was treated with neither antibody nor hyperthermia (the control sample).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28453502", "locator": "sections[3] \"The ChIP-seq dataset\" paragraph 2", "quote": "In this dataset, there were 3 samples of OS cell: one was treated with both anti-HSF1 antibody and heat shocked for 10 min, another was treated with anti-HSF1 antibody and was heat shocked for 20 min, and the last was treated with neither antibody nor hyperthermia (the control sample)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used MACS2 to screen HSF1-binding sites and DAVID for GO and KEGG enrichment analysis, with the GSE60984 HSF1 ChIP-seq dataset downloaded from the Gene Expression Omnibus database; 13,657 miRNA–gene-regulated pairs were identified in the resulting network.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28453502", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The HSF1 ChIP-seq dataset of GSE60984 was downloaded from the Gene Expressed Omnibus (GEO) database."}, {"asset": "source:pmid:28453502", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The HSF1-binding sites were screened by MACS2 in OS cells after 10 and 20 min of hyperthermia, and they were annotated using the ChIPseeker package."}, {"asset": "source:pmid:28453502", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the overlaps."}, {"asset": "source:pmid:28453502", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "1880 and 1283 genes of promoter regions were obtained in the osteosarcoma cells after 10 and 20 min of hyperthermia, respectively, and 889 of them were overlapped."}, {"asset": "source:pmid:28453502", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "There were 13 657 pairs involved in the miRNA-gene regulated network of the overlaps."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used MACS2 to screen HSF1-binding sites and DAVID for GO and KEGG enrichment analysis, with the GSE60984 HSF1 ChIP-seq dataset downloaded from the Gene Expression Omnibus database; 13,657 miRNA–gene-regulated pairs were identified in the resulting network.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:28453502"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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